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02.25.14

NEWS HIGHLIGHTS Tuesday, February 25, 2014

Online Course in Bioinformatics Algorithms Ranks #1 in International Rating

After all the work they put into the online course they inaugurated in the fall, CSE Prof. Pavel Pevzner and his fellow instructors, Phillip Compeau and Nikolay Vyahhi, have concrete evidence that it was a success beyond the impressive number of people who signed up for the course - over 30,000 in all. According to CourseTalk, which tracks user reviews and ratings for Massive Open Online Courses (MOOCs) on a worldwide basis, the UC San Diego-based course on Bioinformatics Algorithms (Part I) currently ranks #1 among all online courses with ratings. The rankings are based on the course's five-star ranking, and 13 superlative reviews that averaged 4.9 out of 5 points. The course just completed, and students may submit more reviews, so it's difficult to know how long the UC San Diego course will remain #1. The number-two ranked MOOC is an introduction to interactive programming in Python, which, unlike Bioinformatics Algorithms, has much broader appeal because it's a course for beginners. By contrast, students who took Prof. Pevzner's course had to already know how to program in at least one language. Indeed, students gave the UC San Diego course great reviews despite the fact that it was a difficult class, whereas positive student evaluations typically correlate to the ease and fewer hours spent studying. According to Pevzner (pictured below from his video preview on Coursera), the reviewers were asked how many hours per week they worked on the course, and the mean answer was 12 hours and 45 minutes - "way more than we expect from students taking regular UC San Diego classes!"

The reviews on Coursera reflected the appreciation of students who were given access to a variety of new tools developed in connection with the course lecture videos. "Bioinformatics Algorithms includes multiple amazing resources to enhance your class experience," wrote one anonymous reviewer. Specifically, students were given access to Rosalind, a programming resource offering an introduction to Python as well as complex bioinformatics problems, as well as an online textbook. "This is one of the best courses that I've ever taken," said reviewer Eun Cheon Lim, a bioinformatics Ph.D. student at Max Planck Institute, who completed the course. Added another reviewer, Guillermo Garcia, who also completed the course: "Very well organized, very good material and CHALLENGING! I felt very satisfied when finishing the assignments." Looking to the future, Pevzner says the course will run again in Fall 2014, and it will be followed by Bioinformatics Algorithms (Part 2), which is currently under development.

Teaching Kids to Code: CSE Student Featured in San Diego Union-Tribune Article

While she has made it her calling to educate youngsters about computer science, CSE Ph.D. student Sarah Esper (right) is taking a fresh and entrepreneurial approach to making that happen, and she has lofty ambitions. In an article that appeared Feb. 24 in the San Diego Union-Tribune ("Start early to program your next career"), Esper is quoted as saying that "we'd like San Diego to become the hub of really great computer science education." The CSE student -- who expects to receive her doctorate in Fall 2014 -- was featured for the work she is doing as an instructor for UC San Diego Extension's K-16 Programs, for which she teaches the basics of computer science to local high school, middle school and elementary students.

Apart from the work she does for Extension, Esper hopes to have her biggest impact through ThoughtSTEM, a company she co-founded with fellow Ph.D. students Stephen Foster and Lindsey Handley. The company does some training of computer science teachers, but its primary mandate is to enroll and teach computer science to children ages 8 to 18. ThoughtSTEM hires approximately 20 UC San Diego undergraduates each year to teach computer science courses to kids all around San Diego, or to help with developing curriculum and technologies to be used by students who enroll in ThoughtSTEM courses. "Not all of the teachers are CSE alumni," says Esper, "but we do hire a lot from CSE." Esper and Foster also jointly developed an educational software package, called CodeSpells (pictured), which takes an innovative, game-like approach to help young students learn how to write code. "We currently don't do anything with CodeSpells in ThoughtSTEM," says Esper, "but in the fall we hope to offer a ThoughtSTEM course using CodeSpells to teach Java."

CSE students and alumni were among those participating Feb. 20 at the Open Lab Night staged by the Qualcomm Institute's Center of Interdisciplinary Science for Art, Architecture and Archaeology (CISA3) and the CISA3-based NSF five-year IGERT project on engineering and cultural heritage diagnostics. David Srour (right), who earned his B.S. in Computer Science in 2011, is now an IGERT Trainee in the multidisciplinary program that grooms the students to work in cultural heritage or other fields such as scientific visualization. Srour is currently juggling grad school with a programmer analyst position in the Qualcomm Institute's Visualization group, working on virtual-reality software R&D for large-scale display walls.

Another CSE grad student and full-time staff researcher in the Qualcomm Institute is John Mangan (left), who demonstrated his work on using MediaCommons to display cultural heritage in VR environments. Other IGERT Trainees (present and past) demonstrated their research at the Open Lab Night included CSE Ph.D. students Vid Petrovic, David Vanoni, and Andrew Huynh, as well as students from other disciplines including structural engineering, anthropology/archaeology, materials science and engineering, and more.

On display were the latest remote exploration systems, robotics, and the WAVE visualization display (at right), which allowed students to showcase some of the content captured by the IGERT students who spent much of last Fall in Europe, primarily in Florence, with a side expedition to Calabria and delivering lectures in Greece and France.

Faculty candidate and UC Berkeley postdoctoral fellow Ross Girshick will discuss "Learning Architectures for Visual Object Recognition." He will focus on two new systems that have more than doubled the performance of object recognition over the past seven years.

The San Diego Supercomputer Center's Predictive Analytics Center of Excellence (PACE) program kicks off the first of its Data Mining Boot Camps for 2014. The two-day course aims to provide the Big Data community with conceptual and hands-on training.

Faculty candidate Michael Carbin, a Ph.D. candidate from MIT, will present a public seminar on "Verified Approximate Computing." He will present Rely, a program verification and analysis system for answering fundamental questions arising when manipulating an application that implements an approximate computation.

"What Is Design?" is the question that Cognitive Science emeritus professor Donald Norman will attempt to answer in a Distinguished Lecture that is part of the Design at Large series organized by CSE Prof. Scott Klemmer. "Design should be a wonderful ﬁt within the university," says Norman, and "that is the challenge."

Big data has forced databases to change from a monolithic architecture to a composition of computer and storage engines running in one or more multi-tenant clusters. CSE Distinguished Lecturer Shivnath Babu of Duke University will talk about "DBMS+: The Management System for Next-Generation Databases."

Stanford University postdoctoral fellow Dafna Shahaf, a CSE faculty candidate, will talk about "The Aha! Moment: From Data to Insight." She will explain two methods that help users acquire insight efficiently across multiple domains.

UC San Diego Extension and UC-TV are organizing a conference on "UCSD Big Data at Work," primarily to serve the campus and San Diego communities with information about the Big Data challenge to existing industries, and the most valuable future jobs in the Big Data sector. Speakers on the program include CSE Prof. Stefan Savage (pictured), SDSC Director Mike Norman, Calit2 Director and CSE Prof. Larry Smarr, among others.

FACULTY GPS

Park City, UT -- In a town best known for its slopes and the Sundance film festival, CSE Prof. Larry Smarr will be in Park City March 7 to deliver a talk on "Virtual Reality, Self-Diagnostics and Healthcare." It's part of the Future in Review lecture series organized by the Strategic News Service and hosted by the Park City Institute, which is trying to attract more than just skiers and film buffs.

Orlando, FL -- On Sunday, Feb. 23, CSE Prof. Ryan Kastner was among the experts from industry, government and academe participating in an all-day symposium in Orlando on "Medical Device Security Risks and Challenges: A Multidisciplinary Response." He spoke during a session on malware, hacking and other fundamentals of technical risk. Kastner's presentation was titled, "Provably Secure Medical Devices."

Have a notice about upcoming travel to conferences, etc., for the Faculty GPS column in our weekly CSE Newsletter? Be sure to let us know! Email Doug Ramsey at dramsey@ucsd.edu.